I found a way to set it using Terminal:
osascript -l JavaScript <<EndOfScript
ObjC.import("LaunchServices")
$.LSSetDefaultHandlerForURLScheme(ObjC.wrap("tel"), ObjC.wrap("com.apple.mobilephone"))
EndOfScript
Replace "tel" with the type of URL to handle, and "com.apple.mobilephone" with the identifier of the app to handle those URLs.
To find the identifier of an app, run:
osascript -e 'id of app "Phone"'
replacing "Phone" with desired app name. F.e. "Safari" or "Safari.app".
Topic:
App & System Services
SubTopic:
General
Tags: